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bioperl-0.05
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Changes for version 0.05 - 1999-04-25

  • Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more.
  • The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object
  • The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases
  • The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI
  • The scripts/ directory, where industrial strength scripts are put has been started.
  • Many changes - a better distribution all round.

Documentation

Notes
bioperl
Bioperl
Coordinated OOP-Perl Modules for Biology
bpfetch.pl
fetches sequences from bioperl indexed databases
bpindex.pl
indexes files for use by bpfetch

Modules

Bio::DB::Ace
Database object interface to ACeDB servers
Bio::DB::BioSeqI
Abstract interface for a sequence database
Bio::DB::GenBank
Database object interface to GenBank
Bio::DB::GenPept
Database object interface to GenPept
Bio::Index::Abstract
Abstract interface for indexing a flat file
Bio::Index::EMBL
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Bio::Index::Fasta
Interface for indexing (multiple) fasta files
Bio::Index::SwissPfam
Interface for indexing swisspfam files
Bio::Parse
The Bioperl ReadSeq interface
Bio::Root::Err
Exception class for Perl 5 objects
Bio::Root::IOManager
Input and output manager for Perl5 objects.
Bio::Root::Object
A core Perl 5 object.
Bio::Root::Utilities
General-purpose utility module
Bio::Root::Vector
Interface for managing linked lists of Perl5 objects.
Bio::Root::Xref
A generic cross-reference object.
Bio::SearchDist
A perl wrapper around Sean Eddy's histogram object
Bio::Seq
bioperl sequence object
Bio::SeqIO
Handler for SeqIO Formats
Bio::SeqIO::EMBL
EMBL sequence input/output stream
Bio::SeqIO::Fasta
Fasta sequence input/output stream
Bio::SeqIO::GCG
Raw sequence input/output stream
Bio::SeqIO::Handler
Handler of the SeqIO classes for tieing to filehandles
Bio::SeqIO::Raw
Raw sequence input/output stream
Bio::SimpleAlign
Multiple alignments held as a set of sequences
Bio::Tools::AlignFactory
Base object for alignment factories
Bio::Tools::Blast
Bioperl BLAST sequence analysis object
Bio::Tools::Blast::HSP
Bioperl BLAST High-Scoring Segment Pair object
Bio::Tools::Blast::HTML
Bioperl Utility module for HTML formatting Blast reports
Bio::Tools::Blast::Run::LocalBlast
Bioperl module for running Blast analyses locally.
Bio::Tools::Blast::Sbjct
Bioperl BLAST "Hit" object
Bio::Tools::Fasta
Bioperl Fasta utility object
Bio::Tools::IUPAC
Generates unique Seq objects from an ambiguous Seq object
Bio::Tools::RestrictionEnzyme
Bioperl object for a restriction endonuclease object.
Bio::Tools::SeqAnal
Bioperl sequence analysis base class.
Bio::Tools::SeqPattern
Bioperl object for a sequence pattern or motif
Bio::Tools::Sigcleave
Bioperl object for sigcleave analysis
Bio::Tools::WWW
Bioperl manager for web resources related to biology.
Bio::Tools::pSW
DESCRIPTION of Object
Bio::UnivAln
Bioperl alignment object

Provides

Bio::Root::Global
in Bio/Root/Global.pm
Bio::Tools::Blast::Run::Webblast
in Bio/Tools/Blast/Run/Webblast.pm
bp_sw
in Compile/SW/bp_sw.pm

Examples

Other files